#!/bin/sh
#PBS -V
#PBS -j oe
#PBS -l nodes=1:ppn=1,mem=1gb,walltime=120:00:00
#PBS -q batch

set -e

SAMPLE1=$1
SAMPLE2=$2
#config_path=$3
#source ${config_path}/config.sh

echo ${SAMPLE1}_${SAMPLE2}

msisensor msi -d ${ref}/microsatellites.list \
-n ${bam_path}/${SAMPLE2}-recal.bam -t ${bam_path}/${SAMPLE1}-recal.bam \
-e ${target_bed} -o ${MSI_path}/${SAMPLE1}_${SAMPLE2} \
-b 1 \
-q 2 -f 0.1 \
2> ${log_path}/${SAMPLE1}_${SAMPLE2}_msi.log

